Mercurial > repos > jjohnson > snpeff_with_dep
annotate snpEff.xml @ 22:4430626bd994
Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 17 Jan 2013 13:00:52 -0600 |
| parents | 1cae7fb31da7 |
| children | 50c1a8ff6c82 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="snpEff" name="SnpEff" version="1.0"> |
| 2 <description>Variant effect and annotation</description> | |
| 3 <!-- | |
| 4 You will need to change the path to wherever your installation is. | |
| 5 You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | |
| 6 <command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> | |
| 7 --> | |
| 8 <requirements> | |
| 20 | 9 <requirement type="package" version="3.1">snpEff</requirement> |
| 0 | 10 </requirements> |
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4430626bd994
Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
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parents:
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11 <command> |
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4430626bd994
Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
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parents:
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12 export SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`; |
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4430626bd994
Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
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changeset
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13 if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ; |
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4430626bd994
Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
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changeset
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14 then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ; |
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4430626bd994
Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
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diff
changeset
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15 fi; |
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4430626bd994
Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
20
diff
changeset
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16 java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> |
| 0 | 17 <inputs> |
| 18 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> | |
| 19 | |
| 20 <param name="inputFormat" type="select" label="Input format"> | |
| 21 <option value="vcf">VCF</option> | |
| 22 <option value="txt">Tabular</option> | |
| 23 <option value="pileup">Pileup</option> | |
| 24 <option value="bed">BED</option> | |
| 25 </param> | |
| 26 | |
| 27 <param name="outputFormat" type="select" label="Output format"> | |
| 28 <option value="txt">Tabular</option> | |
| 29 <option value="vcf">VCF (only if input is VCF)</option> | |
| 30 <option value="bed">BED</option> | |
| 31 <option value="bedAnn">BED Annotations</option> | |
| 32 </param> | |
| 33 | |
| 34 <param name="genomeVersion" type="select" label="Genome"> | |
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4430626bd994
Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
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diff
changeset
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35 <options from_file="snpeffect_genomedb.loc"> |
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4430626bd994
Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
20
diff
changeset
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36 <column name="name" index="1"/> |
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4430626bd994
Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
20
diff
changeset
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37 <column name="value" index="0"/> |
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4430626bd994
Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
Jim Johnson <jj@umn.edu>
parents:
20
diff
changeset
|
38 </options> |
| 0 | 39 </param> |
| 40 | |
| 41 <param name="udLength" type="select" label="Upstream / Downstream length"> | |
| 42 <option value="0">No upstream / downstream intervals (0 bases)</option> | |
| 43 <option value="200">200 bases</option> | |
| 44 <option value="500">500 bases</option> | |
| 45 <option value="1000">1000 bases</option> | |
| 46 <option value="2000">2000 bases</option> | |
| 47 <option value="5000" selected="true">5000 bases</option> | |
| 48 <option value="10000">10000 bases</option> | |
| 49 <option value="20000">20000 bases</option> | |
| 50 </param> | |
| 51 | |
| 52 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes"> | |
| 53 <option value="">No filter (analyze everything)</option> | |
| 54 <option value="-hom">Analyze homozygous sequence changes only </option> | |
| 55 <option value="-het">Analyze heterozygous sequence changes only </option> | |
| 56 </param> | |
| 57 | |
| 58 <param name="filterIn" type="select" display="radio" label="Filter sequence changes"> | |
| 59 <option value="">No filter (analyze everything)</option> | |
| 60 <option value="-del">Analyze deletions only </option> | |
| 61 <option value="-ins">Analyze insertions only </option> | |
| 62 <option value="-nmp">Only MNPs (multiple nucleotide polymorphisms) </option> | |
| 63 <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option> | |
| 64 </param> | |
| 65 | |
| 66 <param name="filterOut" type="select" display="checkboxes" multiple="true" optional="false" value="None" label="Filter output"> | |
| 67 <option value="None" selected="true">None</option> | |
| 68 <option value="downstream">Do not show DOWNSTREAM changes </option> | |
| 69 <option value="intergenic">Do not show INTERGENIC changes </option> | |
| 70 <option value="intron">Do not show INTRON changes </option> | |
| 71 <option value="upstream">Do not show UPSTREAM changes </option> | |
| 72 <option value="utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option> | |
| 73 </param> | |
| 74 | |
| 75 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> | |
| 76 <option value="">Use default (based on input type)</option> | |
| 77 <option value="-0">Force zero-based positions (both input and output)</option> | |
| 78 <option value="-1">Force one-based positions (both input and output)</option> | |
| 79 </param> | |
| 80 </inputs> | |
| 81 <outputs> | |
| 82 <data format="tabular" name="output" > | |
| 83 <change_format> | |
| 84 <when input="outputFormat" value="txt" format="tabular" /> | |
| 85 <when input="outputFormat" value="vcf" format="vcf" /> | |
| 86 <when input="outputFormat" value="bed" format="bed" /> | |
| 87 <when input="outputFormat" value="bedAnn" format="bed" /> | |
| 88 </change_format> | |
| 89 </data> | |
| 90 <data format="html" name="statsFile" /> | |
| 91 </outputs> | |
| 5 | 92 <stdio> |
| 93 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 94 <exit_code range="1:" level="fatal" description="Error" /> | |
| 95 </stdio> | |
| 0 | 96 <help> |
| 97 | |
| 98 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. | |
| 99 | |
| 100 For details about this tool, please go to http://snpEff.sourceforge.net | |
| 101 | |
| 102 </help> | |
| 103 </tool> | |
| 104 |